The bovine genome contains polymorphic microsatellites

Fries, R.; Eggen, Andre A.; Stranzinger, G.

doi:10.1016/0888-7543(90)90301-a

Cited by 67 publications

(29 citation statements)

References 12 publications

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“…Esforços significativos foram empregados para identificar microsatélites em bovinos (Fries et al, 1990;Moore et al, 1994;Vaiman et al, 1994;Stone et al, 1995;Kirkpatrick et al, 1995;Stone et al, 1997;Reed et al, 2001), suínos (Johansson et al, 1992;Miller et al, 1992;Coppieters et al, 1993;Fredholm et al, 1993;Alexander et al, 1996) e eqüinos (Johansson et al, 1992;Marklund et al, 1994;Hopman et al, 1999;Murphie et al 1999;Ruth et al, 1999). Tal metodologia trouxe muitos benefícios, associados, principalmente, às bases moleculares desse tipo de marcador (Tabela 1).…”

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Marcadores SNP: conceitos básicos, aplicações no manejo e no melhoramento animal e perspectivas para o futuro

Caetano

2009

R. Bras. Zootec.

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RESUMO -Os primeiros estudos de identificação, caracterização e utilização de marcadores moleculares para a caracterização de recursos genéticos e geração de ferramentas para o melhoramento animal datam do final da década de 80. Nos últimos 20 anos as tecnologias para geração de dados moleculares passaram por vários ciclos de renovação. A última onda de inovações tecnológicas representa uma verdadeira revolução e trouxe metodologias para identificar e genotipar marcadores SNP (do inglês Single Nucleotide Polimorphism) de maneira massal. Chips de DNA de alta densidade foram criados para genotipar de dezenas de milhares até centenas de milhares de marcadores SNP em um único ensaio. Além disso, outras tecnologias de média densidade permitem também a genotipagem de dezenas a centenas de marcadores, em números elevados de amostras, com altíssima velocidade e automação. Essas novas tecnologias permitiram a geração de novas aplicações, como as metodologias para avaliação genética e seleção com base no Valor Genômico (Genomic Estimated Breeding Value -GEBV). Os métodos estatísticos para avaliação e seleção genômica estão em pleno desenvolvimento, mas a tecnologia já se tornou uma realidade com o lançamento do primeiro sumário de touros para a raça Holandesa com GEBVs para características de produção e qualidade do leite em janeiro de 2009. Além disso, essas tecnologias também trouxeram novas opções para desenvolvimento de testes diagnósticos para confirmação de paternidade, identificação individual, rastreabilidade, etc. Além dessas inovações, as novas tecnologias de genotipagem de marcadores SNP facilitaram também o desenvolvimento de serviços terceirizados de geração de dados, permitindo que qualquer grupo realize pesquisas avançadas, sempre com as tecnologias mais avançadas, sem a necessidade de investimentos em equipamentos.Palavras-chave: marcadores moleculares, Polimorfismo de Base Única, seleção genômica SNP markers: basic concepts, applications in animal breeding and management and perspectives for the future ABSTRACT -The first studies to identify, characterize and use molecular markers to characterize genetic resources and generate tools for animal breeding and management date from the end of the 80s. In the last 20 years the technologies to generate molecular data went through several innovation cycles. The last wave of technological innovations represents a true revolution, bringing methods to identify and genotype SNP (Single Nucleotide Polymorphism) markers in large scale. High density DNA chips were generated to genotype from tens of thousands to hundreds of thousands of SNPs in a single assay. Furthermore, other medium density technologies allow for the genotyping of tens to hundreds of makers, in high numbers of samples, with very high speed and automation. These new technologies allowed for the generation of new applications, such as the methods to genetically evaluate and select animals based on their Genomic Value (Genomic Estimated Breeding Value -GEBV). The statistical methods for genomic evaluatio...

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Marcadores SNP: conceitos básicos, aplicações no manejo e no melhoramento animal e perspectivas para o futuro

Caetano

2009

R. Bras. Zootec.

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“…Compared to other genomic variation, SNPs are the most abundant known so far in animal. The SNPs could be a potential genetic marker and get a higher interest because of the stability and highthroughput automated analysis (Fries et al 1990;Heaton et al 2002). To complement the development of molecular markers on the basis of single or few loci, high throughput genotyping via next generation sequencing (NGS) in the form of array or chip-based markers is more useful.…”

Section: Introductionmentioning

confidence: 99%

Identification of Single Nucleotide Polymorphisms on Cattle Breeds in Indonesia Using Bovine 50k

Lestari

Rijzaani

Satyawan

et al. 2016

Indones. J. Agric. Sci.

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Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmentation, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.[ 3, 4, 5, 7, 13, 17, dan

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“…Since the first description of bovine microsatellite loci in the early 1990s, many bovine microsatellite loci, mostly di-nucleotide repeats, have been identified (Fries et al, 1990;Vaiman et al, 1992;Ma et al, 1996;Reed et al, 2001). With advent and improvement of multiplex PCR methods, the microsatellite markers were extensively used for evaluating differences of cattle breeds and determining population substructures by many laboratories (MacHugh et al, 1998;Beja-Pereira et al, 2003;Freeman et al, 2004;Cymbron et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Forensic Characterization of Four New Bovine Tri-nucleotide Microsatellite Markers in Korean Cattle (Hanwoo)

Sim¹,

Na²,

Lee

2013

Journal of Animal Science and Technology

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We identified four new bovine tri-nucleotide microsatellite loci and analyzed their sequence structures and genetic parameters in 105 randomly selected Korean cattle (Hanwoo). Allele numbers of the loci B17S0808, B15S6253, B8S7996, and B17S4998 were 10, 11, 12, and 29, respectively. These alleles contained a simple or compound repeat sequences with some variations. Allele distributions of all these loci were in Hardy-Weinberg equilibrium (P > 0.05). Observed heterozygosity and expected heterozygosity ranged from 0.54 (B15S6253) to 0.92 (B17S4998) and from 0.599 (B15S6253) to 0.968 (B17S4998), respectively, and two measures of heterozygosity at each locus were highly correlated. Polymorphism information content (PIC) for these 4 loci ranged from 0.551 (B15S6253) to 0.932 (B17S4998), which means that all these loci are highly informative (PIC > 0.5). Other genetic parameters, power of discrimination (PD) and probability of exclusion (PE) ranged from 0.783 (B15S6253) to 0.984 (B17S4998) and from 0.210 (B15S6253) to 0.782 (B17S4998), respectively. Their combined PD and PE values were 0.9999968 and 0.98005176, respectively. Capillary electrophoresis revealed that average peak height ratio for a stutter was 13.89% at B17S0808, 26.67% at B15S6253, 9.09% at B8S7996, and 43.75% at B17S4998. Although the degree of genetic variability of the locus B15S6253 was relatively low among these four microsatellite markers, their favorable parameters and low peak height ratios for stutters indicate that these four new tri-nucleotide microsatellite loci could be useful multiplex PCR markers for the forensic and population genetic studies in cattle including Korean native breed.

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The bovine genome contains polymorphic microsatellites

Cited by 67 publications

References 12 publications

Marcadores SNP: conceitos básicos, aplicações no manejo e no melhoramento animal e perspectivas para o futuro

Marcadores SNP: conceitos básicos, aplicações no manejo e no melhoramento animal e perspectivas para o futuro

Identification of Single Nucleotide Polymorphisms on Cattle Breeds in Indonesia Using Bovine 50k

Forensic Characterization of Four New Bovine Tri-nucleotide Microsatellite Markers in Korean Cattle (Hanwoo)

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